The discrepancy fuelled speculation that Muqtada al-Sadr's supporters and intermediaries acting on behalf of both the interim Iraqi government and al-Sistani were engaged in fierce eleventh hour negotiations.
AFP first reported an al-Sistani spokesman had confirmed the keys to the mosque were delivered to the leading Shia cleric's office in Najaf.
However, in an interview with Aljazeera, al-Sistani aide Hamid al-Khafaf said no keys had been delivered.
Earlier, the Iraqi Interior Ministry said police had entered the revered site and taken about 400 al-Mahdi Army militiamen into custody after al-Sadr's aides symbolically handed control of the site to Iraq's senior Shia religious authorities.
"The Iraqi police are now in control of the shrine, along with the religious authorities," senior Interior Ministry spokesman Sabah Kadhim had said.
Police presence denied
But in an interview with Aljazeera, al-Sadr aide Ahmad al-Shaibani denied police had entered the site and said Kadhim's statement was "laughable".
US troops have been operating
near the Imam Ali mosque
"There were no al-Mahdi Army men in the holy shrine as of this morning - they are all in the old sector of the city and there is intense fighting with US troops there," he told Aljazeera.
Meanwhile, a top US military officer in Iraq said he could not confirm the country's police had taken control of the mosque in Najaf on Friday and added the whereabouts of al-Sadr were unknown.
A US defence official went further and denied Iraqi government claims Iraqi police had entered the shrine.
"Not a lick of truth to it," said the official, who spoke on condition of anonymity. "We are still outside of the shrine, and so are the Iraqi police."
Al-Sadr aide al-Shaibani told Aljazeera hours earlier that control of the religious site had been given to representatives of the country's most senior Shia figure.
"The keys of the Imam Ali shrine have been handed over to representatives of the Shia highest religious authority, Ayat Allah Ali al-Sistani," he said.
"This step means the administration of the Imam Ali mausoleum has been submitted to the religious authority in the city," he added.
The handover comes after two days of dire warnings by the Iraqi interim government that al-Sadr's militia should withdraw from Najaf and disband, or face a decisive military assault.
"The keys of the Imam Ali shrine have been handed over to representatives of the Shia highest religious authority, Ayat Allah Ali al-Sistani"
Al-Sadr aide Ahmad al-Shaibani
Fighting in the area has been fierce. At least 77 Iraqis have been killed and 70 wounded in fighting in Najaf over the past 24 hours, Iraq's Health Ministry said on Friday. Six of those killed in Najaf were police hit by a mortar attack.
Najaf awoke to an uneasy calm on Friday - punctuated by occasional gunfire - hours after an overnight US bombing raid shook the historic area of the city.
On Thursday, Iraq's interim Prime Minister Iyad Allawi issued a "final call" to al-Sadr and his fighters to leave the shrine - though he did not mention a deadline.
But the US-backed prime minister has faced a dilemma in trying to oust the al-Mahdi Army from their entrenched position.
The site is widely revered by Muslims, especially Shia believers. An assault - particularly one involving US forces - would risk igniting a dangerous backlash.
US officials have said their troops are unlikely take part in an attack on the mosque site itself - although US marines, tanks and aircraft have been clearly active around the area.
Allawi has issued a 'final call' for
al-Mahdi Army fighters to pull out
Television broadcasts on Friday showed two of the mosque's minarets were marked by shrapnel, while a clock in one of the towers had been damaged.
Earlier on Friday, Aljazeera's correspondent reported that an intense artillery barrage hit the cemetery, the old sectors of the city and buildings around the Imam Ali mosque.
Al-Shaibani told Aljazeera al-Sadr's movement "has not closed the door towards negotiations with the Iraqi government to end fighting in Najaf but it is not ready to surrender".
Asked earlier whether fighters of the al-Mahdi Army would leave the shrine if a deal were struck, al-Shaibani said: "Any fighter who wants to enter it will have to leave his weapon outside."
The Shia militiamen had been running the Imam Ali shrine since an earlier uprising in April.